Project Summary CLEC16A gene variation has been associated with type 1 diabetes, multiple sclerosis, systemic lupus erythematosus, celiac disease, Crohn's disease, Addison's disease, primary biliary cirrhosis, rheumatoid arthritis, juvenile idiopathic arthritis, alopecia areata and asthma. CLEC16A's association with eleven immune- mediated diseases highlights its fundamental significance to our understanding of human autoimmunity. The goal of the proposed research is to determine the mechanism by which CLEC16A variation impacts immune function. We have recently shown that CLEC16A modifies antigen presentation in thymic epithelial cells. We generated Clec16a knockdown mice in the nonobese diabetic (NOD) model for type 1 diabetes, and showed that Clec16a silencing modified thymic selection and decreased the risk of autoimmune diabetes. CLEC16A participates in autophagy, a process of protein degradation that intersects with the MHC class II compartment where MHC molecules are loaded with peptide antigen. We proposed that CLEC16A's effect on autophagy had a direct impact on MHC class II presentation. Our hypothesis is supported by the recent report that CLEC16A modifies MHC class II trafficking in human cells. CLEC16A variation was shown to affect the expression of DEXI, a gene of unknown function immediately adjacent to CLEC16A. Published data and our own preliminary findings indicate that CLEC16A and DEXI are co-regulated, and that their expression profiles are highly correlated. These observations suggest that the two genes may be functionally related. Therefore, we now aim to study the function of both CLEC16A and DEXI in antigen presentation, and in thymic epithelial cells in particular. To complement functional studies using newly generated mouse models, we will also correlate CLEC16A variation with functional changes in human cells. Using CRISPR / Cas9 genome editing, we will target disease-associated SNPs in human induced pluripotent stem cells (iPSCs). We will use a published protocol to differentiate gene-edited iPSCs into thymic epithelial cells in order to determine how disease-associated CLEC16A variants modify CLEC16A and DEXI expression, and how these gene variants impact the function of human thymic epithelial cells. The proposed research will define the functional link between CLEC16A variation and autoimmunity. We hypothesize that both CLEC16A and DEXI are modifiers of MHC class II presentation by virtue of their function in autophagy. How a change in the expression of these two genes affects the quality and quantity of peptides presented by MHC class II molecules, particularly in thymic epithelial cells, is a question of critical importance to our understanding of the genetic predisposition to autoimmune disease. Ultimately, better knowledge of factors that modify MHC II presentation will help in the design of therapies to prevent or halt autoimmunity.